Ben Barres had just finished giving a seminar at the prestigious Whitehead Institute for Biomedical Research 10 years ago, describing to scientists from the Massachusetts Institute of Technology, Harvard and other top institutions his discoveries about nerve cells called glia. As the applause died down, a friend later told him, one scientist turned to another and remarked what a great seminar it had been, adding, "Ben Barres's work is much better than his sister's."

There was only one problem. Prof. Barres, then as now a professor of neurobiology at Stanford University, doesn't have a sister in science. The Barbara Barres the man remembered was Ben.

Prof. Barres is transgendered, having completed the treatments that made him fully male 10 years ago. The Whitehead talk was his first as a man, so the research he was presenting was done as Barbara.

Being first a female scientist and then a male scientist has given Prof. Barres a unique perspective on the debate over why women are so rare at the highest levels of academic science and math: He has experienced personally how each is treated by colleagues, mentors and rivals.

Based on those experiences, as well as research on gender differences, Prof. Barres begs to differ with what he calls "the Larry Summers Hypothesis," named for the former Harvard president who attributed the paucity of top women scientists to lack of "intrinsic aptitude." In a commentary in today's issue of the journal Nature, he writes that "the reason women are not advancing [in science] is discrimination" and the "Summers Hypothesis amounts to nothing more than blaming the victim."

In his remarks at an economics conference in January 2005, Mr. Summers said "socialization" is probably a trivial reason for the low number of top female mathematicians and scientists. But Prof. Barres, who as Barbara received the subtle and not-so-subtle hints that steer smart girls away from science, doesn't see it that way. The top science and math student in her New Jersey high school, she was advised by her guidance counselor to go to a local college rather than apply to MIT. She applied anyway and was admitted.

As an MIT undergraduate, Barbara was one of the only women in a large math class, and the only student to solve a particularly tough problem. The professor "told me my boyfriend must have solved it for me," recalls Prof. Barres, 51 years old, in an interview. "If boys were raised to feel that they can't be good at mathematics, there would be very few who were."

Although Barbara Barres was a top student at MIT, "nearly every lab head I asked refused to let me do my thesis research" with him, Prof. Barres says. "Most of my male friends had their first choice of labs. And I am still disappointed about the prestigious fellowship I lost to a male student when I was a Ph.D. student," even though the rival had published one prominent paper and she had six.

As a neuroscientist, Prof. Barres is also skeptical of the claim that differences between male and female brains might explain the preponderance of men in math and science. For one thing, he says, the studies don't adequately address whether those differences are innate and thus present from birth, or reflect the different experiences that men and women have. Harvard psychologist Steven Pinker, who defends the Summers Hypothesis, acknowledges that the existence of gender differences in values, preferences and aptitudes "does not mean that they are innate."

The biggest recent revolution in neuroscience has been the discovery of the brain's "plasticity," or ability to change structure and function in response to experiences. "It's not hard to believe that differences between the brains of male and female adults have nothing to do with genes or the Y chromosome but may be the biological expression of different social settings," says biologist Joan Roughgarden of Stanford, who completed her own transgender transition in 1998.

Jonathan Roughgarden's colleagues and rivals took his intelligence for granted, Joan says. But Joan has had "to establish competence to an extent that men never have to. They're assumed to be competent until proven otherwise, whereas a woman is assumed to be incompetent until she proves otherwise. I remember going on a drive with a man. He assumed I couldn't read a map."

Actually, Ben Barres says there may be something to the stereotype that men are better map readers. The testosterone he received to become male improved his spatial abilities, he writes in Nature, though "I still get lost every time I drive."

Still, there is little evidence that lack of testosterone or anything unique to male biology is the main factor keeping women from the top ranks of science and math, says Prof. Barres, a view that is widely held among scientists who study the issue. Although more men than women in the U.S. score in the stratosphere on math tests, there is no such difference in Japan, and in Iceland the situation is flipped, with more women than men scoring at the very top.

"That seems more like 'socialization' than any difference in innate abilities to me," geneticist Gregory Petsko of Brandeis University wrote last year. In any case, except in a few specialized fields like theoretical physics, there is little correlation between math scores and who becomes a scientist.

Some supporters of the Summers Hypothesis suggest that temperament, not ability, holds women back in science: They are innately less competitive. Prof. Barres's experience suggests that if women are less competitive, it is not because of anything innate but because that trait has been beaten out of them.

"Female scientists who are competitive or assertive are generally ostracized by their male colleagues," he says. In any case, he argues, "an aggressive competitive spirit" matters less to scientific success than curiosity, perseverance and self-confidence.

Women doubt their abilities more than men do, say scientists who have mentored scores of each. "Almost without exception, the talented women I have known have believed they had less ability than they actually had," Prof. Petsko wrote. "And almost without exception, the talented men I have known believed they had more."

Which may account for what Prof. Barres calls the main difference he has noticed since changing sex. "People who do not know I am transgendered treat me with much more respect," he says. "I can even complete a whole sentence without being interrupted by a man."